From 8ba5d1edef7fd81672b6a8239e10c329d930a603 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Florian=20G=C3=A4rber?= <florian.gaerber@uni-hamburg.de>
Date: Tue, 27 Aug 2024 13:06:20 +0200
Subject: [PATCH] feat: Add round_digits parameter to MAA

Refs: #15
---
 DESCRIPTION                  |  2 +-
 NEWS.md                      |  4 ++++
 R/MeanAdjustedAgreement.R    | 20 +++++++++++---------
 R/meanAdjAgree.R             | 10 ++++++----
 man/MeanAdjustedAgreement.Rd | 29 ++++++++++++++---------------
 man/mean.index.Rd            |  2 +-
 man/meanAdjAgree.Rd          | 19 ++++++++++---------
 7 files changed, 47 insertions(+), 39 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 41b6714..cd7ad58 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: RFSurrogates
 Title: Surrogate Minimal Depth Variable Importance
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: c(
     person("Stephan", "Seifert", , "stephan.seifert@uni-hamburg.de", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2567-5728")),
diff --git a/NEWS.md b/NEWS.md
index d05eb8e..476b500 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# RFSurrogates 0.4.2
+
+- Added new optional parameter to `MeanAdjustedAgreement` and `meanAdjAgree`: `round_digits` defaulting to 2. This offers the same behaviour as before, but allows rounding to different amounts of decimal places if desired.
+
 # RFSurrogates 0.4.1
 
 - Fix `SurrogateMinimalDepth`'s result `$selected` returning modified names (#13)
diff --git a/R/MeanAdjustedAgreement.R b/R/MeanAdjustedAgreement.R
index 23bddf0..49ba341 100644
--- a/R/MeanAdjustedAgreement.R
+++ b/R/MeanAdjustedAgreement.R
@@ -11,6 +11,7 @@
 #' @param candidates Vector of variable names that **are candidates to be related to the variables**. (Default: All variables used to create the random forest.)
 #' @param related (Default: TRUE) Whether related variables should be identified.
 #' @param num.threads (Default: 1) Number of threads used for determination of relations.
+#' @param round_digits (Default: 2) Round mean adjusted agreement to this many digits.
 #'
 #' @return A `MeanAdjustedAgreement` list object:
 #'  * `RFS`: The original [RandomForestSurrogates()] object.
@@ -43,13 +44,13 @@
 #' @keywords varrel
 #' @export
 MeanAdjustedAgreement <- function(
-  RFS,
-  t = 5,
-  variables = RFS$ranger$forest$independent.variable.names,
-  candidates = RFS$ranger$forest$independent.variable.names,
-  related = TRUE,
-  num.threads = 1
-) {
+    RFS,
+    t = 5,
+    variables = RFS$ranger$forest$independent.variable.names,
+    candidates = RFS$ranger$forest$independent.variable.names,
+    related = TRUE,
+    num.threads = 1,
+    round_digits = 2) {
   if (!inherits(RFS, "RandomForestSurrogates")) {
     stop("`RFS` must be a `RandomForestSurrogates` object.")
   }
@@ -73,10 +74,11 @@ MeanAdjustedAgreement <- function(
     t = t,
     s.a = s$s.a,
     select.var = related,
-    num.threads = num.threads
+    num.threads = num.threads,
+    round_digits = round_digits
   )
 
-  results = list(
+  results <- list(
     RFS = RFS,
     relations = maa$surr.res,
     threshold = maa$threshold
diff --git a/R/meanAdjAgree.R b/R/meanAdjAgree.R
index e5f3743..cf96a06 100644
--- a/R/meanAdjAgree.R
+++ b/R/meanAdjAgree.R
@@ -10,6 +10,7 @@
 #' @param s.a average number of surrogate variables (ideally calculated by count.surrogates function).
 #' @param select.var set False if only relations should be calculated and no related variables should be selected.
 #' @param num.threads number of threads used for parallel execution. Default is number of CPUs available.
+#' @param round_digits (Default: 2) Round mean adjusted agreement to this many digits in [mean.index].
 #'
 #' @returns A list containing:
 #'  * `variables`: the variables to which relations are investigated
@@ -18,7 +19,7 @@
 #'  * `surr.var`: binary matrix showing if the variables are related (1) or non-related (0) with variables in rows and candidates in columns.
 #'
 #' @export
-meanAdjAgree <- function(trees, variables, allvariables, candidates, t, s.a, select.var, num.threads = NULL) {
+meanAdjAgree <- function(trees, variables, allvariables, candidates, t, s.a, select.var, num.threads = NULL, round_digits = 2) {
   num.trees <- length(trees)
   index.variables <- match(variables, allvariables)
   index.candidates <- match(candidates, allvariables)
@@ -39,7 +40,8 @@ meanAdjAgree <- function(trees, variables, allvariables, candidates, t, s.a, sel
       1:length(index.variables),
       mean.index,
       list.res,
-      index.variables
+      index.variables,
+      round_digits = round_digits
     )),
     ncol = length(candidates), nrow = length(variables), byrow = TRUE
   )
@@ -64,9 +66,9 @@ meanAdjAgree <- function(trees, variables, allvariables, candidates, t, s.a, sel
 #' This is an internal function
 #'
 #' @keywords internal
-mean.index <- function(i, list.res, index.variables) {
+mean.index <- function(i, list.res, index.variables, round_digits = 2) {
   list <- list.res[which(names(list.res) == index.variables[i])]
-  mean.list <- round(Reduce("+", list) / length(list), 2)
+  mean.list <- round(Reduce("+", list) / length(list), digits = round_digits)
   if (length(mean.list) > 0) {
     return(mean.list)
   } else {
diff --git a/man/MeanAdjustedAgreement.Rd b/man/MeanAdjustedAgreement.Rd
index b342cb9..fb081e0 100644
--- a/man/MeanAdjustedAgreement.Rd
+++ b/man/MeanAdjustedAgreement.Rd
@@ -10,34 +10,33 @@ MeanAdjustedAgreement(
   variables = RFS$ranger$forest$independent.variable.names,
   candidates = RFS$ranger$forest$independent.variable.names,
   related = TRUE,
-  num.threads = 1
+  num.threads = 1,
+  round_digits = 2
 )
 }
 \arguments{
-\item{RFS}{A \code{\link[=RandomForestSurrogates]{RandomForestSurrogates()}} object.}
+\item{RFS}{A [RandomForestSurrogates()] object.}
 
 \item{t}{(Default: 5) Used to calculate threshold.}
 
-\item{variables}{Vector of variable names for \strong{which related variables should be searched}. (Default: All variables used to create the random forest.)}
+\item{variables}{Vector of variable names for **which related variables should be searched**. (Default: All variables used to create the random forest.)}
 
-\item{candidates}{Vector of variable names that \strong{are candidates to be related to the variables}. (Default: All variables used to create the random forest.)}
+\item{candidates}{Vector of variable names that **are candidates to be related to the variables**. (Default: All variables used to create the random forest.)}
 
 \item{related}{(Default: TRUE) Whether related variables should be identified.}
 
 \item{num.threads}{(Default: 1) Number of threads used for determination of relations.}
+
+\item{round_digits}{(Default: 2) Round mean adjusted agreement to this many digits.}
 }
 \value{
-A \code{MeanAdjustedAgreement} list object:
-\itemize{
-\item \code{RFS}: The original \code{\link[=RandomForestSurrogates]{RandomForestSurrogates()}} object.
-\item \code{relations}: Matrix with mean adjusted agreement values
-\itemize{
-\item Rows: \code{variables}.
-\item Columns: \code{candidates}.
-}
-\item \code{threshold}: the threshold used to select related variables.
-\item \code{related}: A list of vectors for each \code{variable} containing related \code{candidates}. Only present if \code{related = TRUE} (Default).
-}
+A `MeanAdjustedAgreement` list object:
+ * `RFS`: The original [RandomForestSurrogates()] object.
+ * `relations`: Matrix with mean adjusted agreement values
+   * Rows: `variables`.
+   * Columns: `candidates`.
+ * `threshold`: the threshold used to select related variables.
+ * `related`: A list of vectors for each `variable` containing related `candidates`. Only present if `related = TRUE` (Default).
 }
 \description{
 This function uses the mean adjusted agreement to select variables that are related to a defined variable using a threshold T.
diff --git a/man/mean.index.Rd b/man/mean.index.Rd
index 098eaf1..9d2cf26 100644
--- a/man/mean.index.Rd
+++ b/man/mean.index.Rd
@@ -4,7 +4,7 @@
 \alias{mean.index}
 \title{mean.index}
 \usage{
-\method{mean}{index}(i, list.res, index.variables)
+\method{mean}{index}(i, list.res, index.variables, round_digits = 2)
 }
 \description{
 This is an internal function
diff --git a/man/meanAdjAgree.Rd b/man/meanAdjAgree.Rd
index cb1f03c..61b1c39 100644
--- a/man/meanAdjAgree.Rd
+++ b/man/meanAdjAgree.Rd
@@ -12,11 +12,12 @@ meanAdjAgree(
   t,
   s.a,
   select.var,
-  num.threads = NULL
+  num.threads = NULL,
+  round_digits = 2
 )
 }
 \arguments{
-\item{trees}{list of trees created by \code{\link[=getTreeranger]{getTreeranger()}}, \code{\link[=addLayer]{addLayer()}} and \code{\link[=addSurrogates]{addSurrogates()}}.}
+\item{trees}{list of trees created by [getTreeranger()], [addLayer()] and [addSurrogates()].}
 
 \item{variables}{vector of variable names.}
 
@@ -24,22 +25,22 @@ meanAdjAgree(
 
 \item{candidates}{vector of variable names (strings) that are candidates to be related to the variables (has to be contained in allvariables)}
 
-\item{t}{variable to calculate threshold. Used if \code{select.var = TRUE}.}
+\item{t}{variable to calculate threshold. Used if `select.var = TRUE`.}
 
 \item{s.a}{average number of surrogate variables (ideally calculated by count.surrogates function).}
 
 \item{select.var}{set False if only relations should be calculated and no related variables should be selected.}
 
 \item{num.threads}{number of threads used for parallel execution. Default is number of CPUs available.}
+
+\item{round_digits}{(Default: 2) Round mean adjusted agreement to this many digits in [mean.index].}
 }
 \value{
 A list containing:
-\itemize{
-\item \code{variables}: the variables to which relations are investigated
-\item \code{surr.res}: matrix with mean adjusted agreement values and variables investigated in rows and candidate variables in columns
-\item \code{threshold}: the threshold used to create surr.var from surr.res
-\item \code{surr.var}: binary matrix showing if the variables are related (1) or non-related (0) with variables in rows and candidates in columns.
-}
+ * `variables`: the variables to which relations are investigated
+ * `surr.res`: matrix with mean adjusted agreement values and variables investigated in rows and candidate variables in columns
+ * `threshold`: the threshold used to create surr.var from surr.res
+ * `surr.var`: binary matrix showing if the variables are related (1) or non-related (0) with variables in rows and candidates in columns.
 }
 \description{
 This is the main function of var.relations function.
-- 
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